Mulberry (Morus indica L.) is an important tree crop being exploited for feeding the silk-producing insect Bombyx mori L. In order to identify parents suitable for breeding to raise high-yielding varieties for the non-traditional areas of Kerala, India and also to identify markers associated with leaf yield attributing traits, the present study was undertaken with 44 mulberry genotypes. Variability on morphobiometric traits and molecular markers, generated with 12 selected ISSR primers, was estimated. Significant differences between genotypes were observed for all the traits. The dendrogram generated with morpho-biometric characters clustered the genotypes into three distinct groups and one isolate, while the same using Inter simple sequence repeat (ISSR) markers clustered the genotypes into five groups and six isolates. The greater resolving power of the ISSR markers was evident form the dendrograms. Using step-wise multiple regression analysis, a number of markers associated with number of branches, total shoot length, leaf weight, internodal distance, leaf chlorophyll, protein, leaf moisture percentage were identified. These markers could be of much use in Marker assisted selection (MAS) breeding programmes in mulberry, especially when no genetic information in terms of linkage maps and Quantitative Trait Locis (QTLs) is available a plant with high heterozygosity and a long juvenile period.